Abstract
BackgroundDNA methylation plays a key role in the regulation of gene expression and carcinogenesis. Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation. Until now, only a few software tools have focused on virus integration using bisulfite sequencing data.FindingsWe have developed a new and easy-to-use software tool, named BS-virus-finder (BSVF, RRID:SCR_015727), to detect viral integration breakpoints in whole human genomes. The tool is hosted at https://github.com/BGI-SZ/BSVF.ConclusionsBS-virus-finder demonstrates high sensitivity and specificity. It is useful in epigenetic studies and to reveal the relationship between viral integration and DNA methylation. BS-virus-finder is the first software tool to detect virus integration loci by using bisulfite sequencing data.
Highlights
DNA methylation plays a crucial role in many areas including development [1, 2] and X chromosome inactivation [3] by regulating genetic imprinting and epigenetic modification without altering DNA sequences
Bisulfite sequencing studies mainly focus on calling single nucleotide polymorphism, different methylation region, and find allele-specific DNA methylation
We consider breakpoints predicted by our software tool correctly identified if they are within 10 bp of a real breakpoint (Fig. S2)
Summary
DNA methylation plays a crucial role in many areas including development [1, 2] and X chromosome inactivation [3] by regulating genetic imprinting and epigenetic modification without altering DNA sequences. BS technology can investigate DNA methylation changes with single-base accuracy. Bisulfite treatment introduces specific changes in the DNA sequence that depend on the methylation status of individual cytosine residues, yielding single-nucleotide resolution information about the methylation status of a segment of DNA (Fig. 1). Whole-genome-based bisulfite sequencing (WGBS) has been developed to detect DNA methylation. Whole-genome BS data can be analyzed to investigate the sequence mapping and alignment via BSMAP [10], Bismark [11], and bwa-meth [12], to detect different methylation regions (DMRs) via the software QDMR [13], DMAP [14], and SMAP [15], to identify single nucleotide polymorphisms (SNPs) via BS-SNPer [16] and Bis-SNP [17], and to find allele-specific DNA methylation via SMAP [15] and Methy-Pipe [18].
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